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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATGgtaacgtctctttaacgacgtcagacgcaatctgcatttcttcactatgttgcaaagctttgagaatctacagtctgggactcatggcgggttctgtcgatgtgccttggaacttacatgcgtccatgttgtatgttggttggttcttgaacatgatgtttcagcaattgaggaatcttatgattgtcatgcag

Basic information

species Physcomitrella patens
transcript PP1S79_180V6.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 3
CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATGgtaacgtctc-tttaacgacgtcagacgcaatctgcatttcttcactatgttgcaaagctttgagaatctacagtctgggactcatggcgggttctgtcgatgtgccttggaacttacatgcgtccatgttgtatgttggttggttcttgaacatgatgtttcagcaattgaggaatcttatgattgtcatgcag
|| || || |||||||| || ||| |||| || ||||||||||| ||||||||||||||||||||| | ||| | |   |  ||      |  |||| |||   |  ||  | ||  |||||   |  ||| | | | ||||| |    |  | || ||  ||| |        ||| | |    |   |||| || |   |||   | |||  ||| ||  || |  |||||    ||   |   |  | || |||
CGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTACATCCAACAGAGCCATGgtaatgcctcctctgctgctgttgttttctttctgaattcgattcct--gatgtgaagct---aacatc-ataat-tgggaatatctgtagtttgtgaggatttagtc----actaatagtgatgtttgttatacg--agtttactgttgg-catcat--ttaattaattgcttcatgcaaccttgttaattcag

upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 3
CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATGgtaacgtctc-tttaacgacgtcagacgcaatctgcatttcttcactatgttgcaaagctttgagaatctacagtctgggactcatggcgggttctgtcgatgtgccttggaacttacatgcgtccatgttgtatgttggttggttcttgaacatgatgtttcagcaattgaggaatcttatgattgtcatgcag
|| || || |||||||| || ||| |||| || ||||||||||| ||||||||||||||||||||| | ||| | |   |  ||         |||| |||   |   |||| ||  |||||   |  ||| | | | ||||| |    |  | || ||  ||| |        ||| | |    |   |||||||      ||   | |||  ||| ||  || |  |||||    ||   |   |  | || |||
CGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATGgtaatgcctcctctgctgctgttgttttgtttctgaattcaatt--tatgatgtgaagct---aacatc-ataat-tgggaatatctgtagtttgtgaggatttagtc----actaataccgatgtttgttgtacaac--tttactgttgg-catcat--ttaattaattgcttgatgcaaacttgttaattcag

upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 3
CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATGgtaacgtctctttaacgacgtcagacgcaatctgc-atttcttcactatgttgcaaagctttgagaatctacagtctgggactcatggcgggttctgtcgatgtgccttggaacttacatgcgtccatgttgtatgttggttggttcttgaacatgatgtttcagcaattgaggaatcttatgattgtcatgcag
|| || || |||||||| || ||| |||| |||| ||||||||| ||||||||||| ||||||||| | ||  |      | |  |  |   | ||  ||||  ||||||        |  | |   ||| ||         | | ||  |    | | |  || ||      |                                                                                   
CGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATGgtaatgccttat------ccttggttgtgttttgtgattttatcacta-------gaattattttaatatatgaagctaaatttataaccacctttat-aatttgttgctcatt---------------------------------------------------------------------------------

upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 3
CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATGgtaacgtctctttaacgacgtcagacgcaatctgc-atttcttcactatgttgcaaagctttgagaatctacagtctgggactcatggcgggttctgtcgatgtgccttggaacttacatgcgtccatgttgtatgttggttggttcttgaacatgatgtttcagcaattgaggaatcttatgattgtcatgcag
|| || || || ||||| || ||| |||| |||| ||||||||| ||||||||||| ||||||||| | ||  |      | |  |  |   | ||  ||||  |||||     | ||   ||| |  || |  |       | | ||  |  | | | |  || |||     |                                                                                   
CGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATGgtaatgccttat------ccttggttgtgctttgtgattttatcact-----ggaattattttaagatatgaaact--aaatttataaccagctttat-aatttgctgctcatt---------------------------------------------------------------------------------

upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 3
CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATGgtaacgtctctttaacgacgt-cagacgcaatctgcatttcttcactatgttgcaaagctttgagaatctacagtctgggactcatggcgggttctgtcgatgtgccttggaacttacatgcgtccatgttgtatgttggttggttcttgaacatgatgtttcagcaattgaggaatcttatgattgtcatgcag
 | ||| | ||||||||||||||| ||||||| | ||||||||||||||| ||||| |||||||||  ||    |  ||   | |   |  | | |       ||   | || | | ||    || ||   || |  |   |  |    |                                                                                                           
AGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATGgtaatttcaagctttcgctttgctttcatacttttgtaccgttatttctgctactaacgactgggatggtaaaaacattggtttgcag-----------------------------------------------------------------------------------------------------------

upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 3
CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATGgtaacgtctctttaacgacgtcagacgcaatctgcatttcttcactatgttgcaaagctttgagaatctacagtctgggactcatggcgggttctgtcgatgtgccttggaacttacatgcgtccatgttgtatgttggttggttcttgaacatgatgtttcagcaattgaggaatcttatgattgtcatgcag
 |||||||||||||||| || ||| |||| || | ||||||||| |||||| | ||||||||||||      | |||     |  | |  ||| |   |   ||     |||| ||||  ||     |  |  |   | |||     | |        | | ||  | |||                                                                                     
AGGAAACTCGCGCAAAGATCAGAGAGAGTAAAATCTGTGGATCTGCATCCATCTGAGCCATGgtaat-----tataatatgtttggccataatttatgtactttt----tgtttcaaattttctctgacttgaa---taggaaatgagacttagatgtttgctggccattgtgg----------------------------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18345941|gb|BJ177984.1|BJ177984
EST:     CAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG                         GATATTATCCAGCTTATATACCGGAAGTCTTCATATTTGGAACTACCAGAA
genomic: CAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATGgtaacgtctc ... tgtcatgcagGATATTATCCAGCTTATATACCGGAAGTCTTCATATTTGGAACTACCAGAA
EST: gi|18374691|gb|BJ206269.1|BJ206269
EST:     CAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG                         GATATTATCCAGCTTATATACCGGAAGTCTTCATATTTGGAACTACCAGAA
genomic: CAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATGgtaacgtctc ... tgtcatgcagGATATTATCCAGCTTATATACCGGAAGTCTTCATATTTGGAACTACCAGAA
EST: gi|18366204|gb|BJ198282.1|BJ198282
EST:     CAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG                         GATATTATCCAGCTTATATACCCGGAAGTCTTCATATTTGGAACTACCAGA
genomic: CAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATGgtaacgtctc ... tgtcatgcagGATATTATCCAGCTTATATA-CCGGAAGTCTTCATATTTGGAACTACCAGA